>>> Building on exopi-3 under biology/hmmer BDEPENDS = [devel/gmake] DIST = [biology/hmmer:hmmer-3.1b2.tar.gz] FULLPKGNAME = hmmer-3.1beta2p0 Avoided depends for gmake-4.4.1 distfiles size=5965253 >>> Running build in biology/hmmer at 1731785093.26 ===> biology/hmmer ===> Building from scratch hmmer-3.1beta2p0 ===> hmmer-3.1beta2p0 depends on: gmake-* -> gmake-4.4.1 ===> Verifying specs: c m pthread ===> found c.100.3 m.10.1 pthread.27.1 ===> Checking files for hmmer-3.1beta2p0 `/exopi-cvs/ports/distfiles/hmmer-3.1b2.tar.gz' is up to date. >> (SHA256) all files: OK ===> Extracting for hmmer-3.1beta2p0 ===> Patching for hmmer-3.1beta2p0 ===> Compiler link: clang -> /usr/bin/clang ===> Compiler link: clang++ -> /usr/bin/clang++ ===> Compiler link: cc -> /usr/bin/cc ===> Compiler link: c++ -> /usr/bin/c++ ===> Generating configure for hmmer-3.1beta2p0 ===> Configuring for hmmer-3.1beta2p0 Using /exopi-obj/pobj/hmmer-3.1beta2/config.site (generated) configure: WARNING: unrecognized options: --disable-silent-rules, --disable-gtk-doc configure: loading site script /exopi-obj/pobj/hmmer-3.1beta2/config.site configure: Configuring HMMER for your system. checking build system type... x86_64-unknown-openbsd7.6 checking host system type... x86_64-unknown-openbsd7.6 configure: Full HMMER source distribution - using full configuration checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... (cached) o checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... none needed checking for C compiler vendor... gnu checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking for a BSD-compatible install... /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c checking how to run the C preprocessor... cc -E checking for C compiler vendor... (cached) gnu checking for cc option to accept ISO C99... none needed checking for cc option to accept ISO Standard C... (cached) none needed checking for ranlib... (cached) ranlib checking for ar... /usr/bin/ar checking whether you have a GNU make... yes, you do; and we assume you will use it! checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for cc option to produce PIC... -fPIC checking whether C compiler accepts -msse2... yes checking compiler support for sse2 cast functions... yes checking whether SSE2 is supported... yes checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes configure: Activating Intel/AMD SSE optimized DP implementation checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for netinet/in.h... (cached) yes checking for sys/param.h... (cached) yes checking for sys/sysctl.h... (cached) yes checking whether byte ordering is bigendian... no checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... (cached) yes checking for mkstemp... (cached) yes checking for popen... (cached) yes checking for strcasecmp... (cached) yes checking for times... (cached) yes checking for getpid... (cached) yes checking for sysctl... (cached) yes checking for sysconf... (cached) yes checking for getcwd... (cached) yes checking for stat... (cached) yes checking for fstat... (cached) yes checking for ntohs... (cached) yes checking for ntohl... yes checking for htons... (cached) yes checking for htonl... (cached) yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating libdivsufsort/Makefile config.status: creating Makefile config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: creating libdivsufsort/divsufsort.h config.status: linking src/impl_sse to src/impl HMMER configuration: compiler: cc -O2 -pipe -msse2 -pthread -fPIC host: x86_64-unknown-openbsd7.6 linker: libraries: DP implementation: sse configure: WARNING: unrecognized options: --disable-silent-rules, --disable-gtk-doc ===> Building for hmmer-3.1beta2p0 gmake -C easel all gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/easel' cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o easel.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/easel.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_alphabet.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_alphabet.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_buffer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_buffer.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_cluster.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_cluster.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_composition.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_composition.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_dirichlet.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_dirichlet.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_distance.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_distance.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_dmatrix.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_dmatrix.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_dmatrix.c:893:15: warning: self-comparison always evaluates to false [-Wtautological-compare] if (A->type != A->type) ESL_EXCEPTION(eslEINVAL, "matrices of different type"); ^ 1 warning generated. cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_exponential.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_exponential.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_fileparser.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_fileparser.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_gamma.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_gamma.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_getopts.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_getopts.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_gev.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_gev.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_gumbel.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_gumbel.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_histogram.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_histogram.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_hmm.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_hmm.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_hyperexp.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_hyperexp.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_keyhash.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_keyhash.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_mem.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_mem.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_minimizer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_minimizer.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_mixgev.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_mixgev.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_mpi.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_mpi.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msa.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msa.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msacluster.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msacluster.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile2.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile2.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_a2m.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_a2m.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_afa.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_afa.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_clustal.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_clustal.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_phylip.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_phylip.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_psiblast.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_psiblast.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_selex.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_selex.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msafile_stockholm.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msafile_stockholm.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msashuffle.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msashuffle.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_msaweight.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_msaweight.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_normal.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_normal.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_paml.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_paml.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_random.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_random.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_randomseq.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_randomseq.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_ratematrix.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_ratematrix.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_recorder.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_recorder.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_regexp.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_regexp.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_rootfinder.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_rootfinder.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_scorematrix.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_scorematrix.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_sq.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sq.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_sqio.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_sqio_ascii.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio_ascii.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_sqio_ncbi.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio_ncbi.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio_ncbi.c:1721:26: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] *ptr = (text) ? '\0' : eslDSQ_SENTINEL; ~ ^~~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/easel.h:309:25: note: expanded from macro 'eslDSQ_SENTINEL' #define eslDSQ_SENTINEL 255 /* sentinel bytes 0,L+1 in a dsq */ ^~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio_ncbi.c:1839:37: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] *ptr = (sq->dsq == NULL) ? '\0' : eslDSQ_SENTINEL; ~ ^~~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/easel.h:309:25: note: expanded from macro 'eslDSQ_SENTINEL' #define eslDSQ_SENTINEL 255 /* sentinel bytes 0,L+1 in a dsq */ ^~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sqio_ncbi.c:2071:26: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] *ptr = (text) ? '\0' : eslDSQ_SENTINEL; ~ ^~~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/easel.h:309:25: note: expanded from macro 'eslDSQ_SENTINEL' #define eslDSQ_SENTINEL 255 /* sentinel bytes 0,L+1 in a dsq */ ^~~ 3 warnings generated. cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_sse.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_sse.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_ssi.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_ssi.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_stack.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_stack.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_stats.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_stats.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_stopwatch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_stopwatch.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_stretchexp.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_stretchexp.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_threads.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_threads.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_translate.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_translate.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_tree.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_tree.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_vectorops.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_vectorops.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_vmx.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_vmx.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_weibull.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_weibull.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_workqueue.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_workqueue.c cc -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -O2 -pipe -pthread -fPIC -msse2 -o esl_wuss.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/esl_wuss.c /usr/bin/ar -r libeasel.a easel.o esl_alphabet.o esl_buffer.o esl_cluster.o esl_composition.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_getopts.o esl_gev.o esl_gumbel.o esl_histogram.o esl_hmm.o esl_hyperexp.o esl_keyhash.o esl_mem.o esl_minimizer.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msafile.o esl_msafile2.o esl_msafile_a2m.o esl_msafile_afa.o esl_msafile_clustal.o esl_msafile_phylip.o esl_msafile_psiblast.o esl_msafile_selex.o esl_msafile_stockholm.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_random.o esl_randomseq.o esl_ratematrix.o esl_recorder.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_sse.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_threads.o esl_translate.o esl_tree.o esl_vectorops.o esl_vmx.o esl_weibull.o esl_workqueue.o esl_wuss.o > /dev/null 2>&1 gmake -C miniapps all gmake[2]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/easel/miniapps' Makefile:121: warning: ignoring prerequisites on suffix rule definition cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-afetch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-afetch.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-afetch esl-afetch.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alimanip.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alimanip.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimanip esl-alimanip.o -leasel -lm ld: warning: esl_alphabet.c(esl_alphabet.o:(esl_alphabet_CreateCustom) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alimap.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alimap.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimap esl-alimap.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alimask.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alimask.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimask esl-alimask.o -leasel -lm ld: warning: esl_msa.c(esl_msa.o:(esl_msa_Copy) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alimerge.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alimerge.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alimerge esl-alimerge.o -leasel -lm ld: warning: esl_msa.c(esl_msa.o:(esl_msa_Copy) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alipid.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alipid.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alipid esl-alipid.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-alistat.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-alistat.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-alistat esl-alistat.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-cluster.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-cluster.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-cluster esl-cluster.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-compalign.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-compalign.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-compalign esl-compalign.o -leasel -lm ld: warning: esl_alphabet.c(esl_alphabet.o:(esl_alphabet_CreateCustom) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-compstruct.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-compstruct.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-compstruct esl-compstruct.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-construct.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-construct.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-construct esl-construct.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-histplot.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-histplot.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-histplot esl-histplot.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-mask.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-mask.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-mask esl-mask.o -leasel -lm ld: warning: esl_getopts.c(esl_getopts.o:(set_option) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-reformat.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-reformat.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-reformat esl-reformat.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-selectn.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-selectn.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-selectn esl-selectn.o -leasel -lm ld: warning: esl_getopts.c(esl_getopts.o:(set_option) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-seqrange.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-seqrange.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-seqrange esl-seqrange.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-seqstat.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-seqstat.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-seqstat esl-seqstat.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_ssi.c(esl_ssi.o:(esl_newssi_Write) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-sfetch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-sfetch.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-sfetch esl-sfetch.o -leasel -lm ld: warning: esl_getopts.c(esl_getopts.o:(set_option) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-shuffle.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-shuffle.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-shuffle esl-shuffle.o -leasel -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-ssdraw.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:2318:39: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] if(esl_FCompare(scl->limits[c+1], SSDRAWINFINITY, eslSMALLX1) == eslOK) { /* max value is infinity, special case */ ~~~~~~~~~~~~ ^~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:32:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:3436:17: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] limits_s[5] = SSDRAWINFINITY; ~ ^~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:32:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:4816:15: warning: implicit conversion from 'int' to 'float' changes value from 987654321 to 987654336 [-Wimplicit-const-int-float-conversion] limits[6] = SSDRAWINFINITY; ~ ^~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-ssdraw.c:32:24: note: expanded from macro 'SSDRAWINFINITY' #define SSDRAWINFINITY 987654321 ^~~~~~~~~ 3 warnings generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-ssdraw esl-ssdraw.o -leasel -lm ld: warning: esl-ssdraw.c(esl-ssdraw.o:(parse_template_file)): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl-ssdraw.c(esl-ssdraw.o:(create_text_legend_for_consensus_sequence)): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-stranslate.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-stranslate.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-stranslate esl-stranslate.o -leasel -lm ld: warning: esl_alphabet.c(esl_alphabet.o:(esl_alphabet_CreateCustom) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/.. -o esl-weight.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/miniapps/esl-weight.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L.. -o esl-weight esl-weight.o -leasel -lm ld: warning: esl_msa.c(esl_msa.o:(esl_msa_Copy) in archive ../libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../libeasel.a): warning: sprintf() is often misused, please use snprintf() gmake[2]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/easel/miniapps' gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/easel' gmake -C libdivsufsort all gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/libdivsufsort' cc -I. -O2 -pipe -pthread -fPIC -o divsufsort.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/libdivsufsort/divsufsort.c /usr/bin/ar rc libdivsufsort.a divsufsort.o gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/libdivsufsort' gmake -C src all gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src' cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o alimask.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/alimask.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o build.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/build.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o cachedb.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/cachedb.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/cachedb.c:223:16: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] *res_ptr++ = eslDSQ_SENTINEL; ~ ^~~~~~~~~~~~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel/easel.h:309:25: note: expanded from macro 'eslDSQ_SENTINEL' #define eslDSQ_SENTINEL 255 /* sentinel bytes 0,L+1 in a dsq */ ^~~ 1 warning generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o emit.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/emit.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o errors.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/errors.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o evalues.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/evalues.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o eweight.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/eweight.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_decoding.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_decoding.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_fwdback.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_fwdback.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_fwdback_chk.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_fwdback_chk.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_fwdback_banded.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_fwdback_banded.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_null2.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_null2.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_msv.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_msv.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_optacc.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_optacc.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_stotrace.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_stotrace.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_viterbi.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_viterbi.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o generic_vtrace.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/generic_vtrace.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o h2_io.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/h2_io.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o heatmap.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/heatmap.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmlogo.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmlogo.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmdmstr.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmdmstr.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmdwrkr.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmdwrkr.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmdutils.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmdutils.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmer.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o logsum.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/logsum.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o modelconfig.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/modelconfig.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o modelstats.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/modelstats.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o mpisupport.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/mpisupport.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o seqmodel.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/seqmodel.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o tracealign.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/tracealign.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_alidisplay.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_alidisplay.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_bg.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_bg.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_builder.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_builder.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_domaindef.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_domaindef.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_gbands.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_gbands.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_gmx.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_gmx.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_gmxb.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_gmxb.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_gmxchk.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_gmxchk.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_hmm.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_hmm.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_hmmcache.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_hmmcache.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_hmmfile.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_hmmfile.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_hmmwindow.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_hmmwindow.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_null3.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_null3.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_pipeline.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_pipeline.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_prior.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_prior.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_profile.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_profile.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_spensemble.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_spensemble.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_tophits.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_tophits.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_trace.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_trace.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o p7_scoredata.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/p7_scoredata.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmpgmd2msa.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmpgmd2msa.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o fm_alphabet.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_alphabet.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o fm_general.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:146:24: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval_bk->lower = abs(fm->C[(int)c]) + occ_l; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:146:24: note: use function 'llabs' instead interval_bk->lower = abs(fm->C[(int)c]) + occ_l; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:147:24: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval_bk->upper = abs(fm->C[(int)c]) + occ_u - 1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:147:24: note: use function 'llabs' instead interval_bk->upper = abs(fm->C[(int)c]) + occ_u - 1; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:171:42: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->lower = interval_bk.lower = abs(fm->C[c]); ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:171:42: note: use function 'llabs' instead interval->lower = interval_bk.lower = abs(fm->C[c]); ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:172:42: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->upper = interval_bk.upper = abs(fm->C[c+1])-1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:172:42: note: use function 'llabs' instead interval->upper = interval_bk.upper = abs(fm->C[c+1])-1; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:197:21: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->lower = abs(fm->C[(int)c]) + count1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:197:21: note: use function 'llabs' instead interval->lower = abs(fm->C[(int)c]) + count1; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:198:21: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->upper = abs(fm->C[(int)c]) + count2 - 1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:198:21: note: use function 'llabs' instead interval->upper = abs(fm->C[(int)c]) + count2 - 1; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:220:22: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->lower = abs(fm->C[(int)c]); ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:220:22: note: use function 'llabs' instead interval->lower = abs(fm->C[(int)c]); ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:221:22: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval->upper = abs(fm->C[(int)c+1])-1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:221:22: note: use function 'llabs' instead interval->upper = abs(fm->C[(int)c+1])-1; ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:572:13: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] prevC = abs(C[i]); ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_general.c:572:13: note: use function 'llabs' instead prevC = abs(C[i]); ^~~ llabs 9 warnings generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o fm_sse.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_sse.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o fm_ssv.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_ssv.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_ssv.c:136:10: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] j += abs(fmf->C[c]); ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_ssv.c:136:10: note: use function 'llabs' instead j += abs(fmf->C[c]); ^~~ llabs /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_ssv.c:464:65: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] interval_f1.upper = interval_f2.upper = interval_bk.upper = abs(fmf->C[i+1])-1; ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/fm_ssv.c:464:65: note: use function 'llabs' instead interval_f1.upper = interval_f2.upper = interval_bk.upper = abs(fmf->C[i+1])-1; ^~~ llabs 2 warnings generated. /usr/bin/ar -r libhmmer.a build.o cachedb.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdwrkr.o hmmdutils.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hmm.o p7_hmmcache.o p7_hmmfile.o p7_hmmwindow.o p7_null3.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 gmake -C impl_sse libhmmer-impl.stamp gmake[2]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src/impl_sse' cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o decoding.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/decoding.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o fwdback.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/fwdback.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o io.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/io.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/io.c:244:12: warning: comparison of array 'hfp->errbuf' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0'; ~~~~~^~~~~~ ~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/io.c:365:12: warning: comparison of array 'hfp->errbuf' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0'; ~~~~~^~~~~~ ~~~~ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/io.c:512:12: warning: comparison of array 'hfp->errbuf' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (hfp->errbuf != NULL) hfp->errbuf[0] = '\0'; ~~~~~^~~~~~ ~~~~ 3 warnings generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o ssvfilter.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/ssvfilter.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/ssvfilter.c:859:27: warning: implicit conversion from 'int' to 'char' changes value from 128 to -128 [-Wconstant-conversion] beginv = _mm_set1_epi8(128); ~~~~~~~~~~~~~ ^~~ 1 warning generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o msvfilter.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/msvfilter.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o null2.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/null2.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o optacc.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/optacc.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o stotrace.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/stotrace.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o vitfilter.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/vitfilter.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o p7_omx.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/p7_omx.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o p7_oprofile.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/p7_oprofile.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I.. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/.. -o mpi.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/mpi.c /usr/bin/ar -r ../libhmmer.a decoding.o fwdback.o io.o ssvfilter.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1 gmake[2]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src/impl_sse' cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm ld: warning: esl_getopts.c(esl_getopts.o:(set_option) in archive ../easel/libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmalign.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmalign.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: esl_ssi.c(esl_ssi.o:(esl_newssi_Write) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmbuild.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmbuild.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm ld: warning: esl_stopwatch.c(esl_stopwatch.o:(esl_stopwatch_Display) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: esl_sq.c(esl_sq.o:(sq_create_from) in archive ../easel/libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmconvert.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmconvert.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmemit.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmemit.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_sqio_ascii.c(esl_sqio_ascii.o:(esl_sqascii_Open) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmfetch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmfetch.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_SetName) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_ssi.c(esl_ssi.o:(esl_newssi_Write) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmpress.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmpress.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm ld: warning: p7_profile.c(p7_profile.o:(p7_profile_Copy) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: esl_dirichlet.c(esl_dirichlet.o:(esl_mixdchlet_Read) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmscan.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmscan.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_SetName) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: p7_hmmfile.c(p7_hmmfile.o:(p7_hmmfile_WriteToString) in archive ./libhmmer.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmsearch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmsearch.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_tophits.c(p7_tophits.o:(p7_tophits_GetMaxPositionLength) in archive ./libhmmer.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmsim.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmsim.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: p7_hmmfile.c(p7_hmmfile.o:(p7_hmmfile_WriteToString) in archive ./libhmmer.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmstat.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmstat.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_ssi.c(esl_ssi.o:(esl_newssi_Write) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o jackhmmer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/jackhmmer.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_stopwatch.c(esl_stopwatch.o:(esl_stopwatch_Display) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o phmmer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/phmmer.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: esl_stopwatch.c(esl_stopwatch.o:(esl_stopwatch_Display) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o nhmmer.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/nhmmer.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm ld: warning: modelconfig.c(modelconfig.o:(p7_ProfileConfig) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_stopwatch.c(esl_stopwatch.o:(esl_stopwatch_Display) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o nhmmscan.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/nhmmscan.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_SetName) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() ld: warning: esl_stopwatch.c(esl_stopwatch.o:(esl_stopwatch_Display) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmpgmd.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmpgmd.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm ld: warning: hmmdmstr.c(hmmdmstr.o:(clientside_loop) in archive ./libhmmer.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: hmmdwrkr.c(hmmdwrkr.o:(process_SearchCmd) in archive ./libhmmer.a): warning: sprintf() is often misused, please use snprintf() ld: warning: p7_hmm.c(p7_hmm.o:(p7_hmm_AppendComlog) in archive ./libhmmer.a): warning: strcat() is almost always misused, please use strlcat() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmc2.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmc2.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm ld: warning: hmmc2.c(hmmc2.o:(main)): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: hmmc2.c(hmmc2.o:(main)): warning: strcat() is almost always misused, please use strlcat() ld: warning: hmmc2.c(hmmc2.o:(main)): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o makehmmerdb.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/makehmmerdb.c cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm ld: warning: makehmmerdb.c(makehmmerdb.o:(main)): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -I../easel -I../libdivsufsort -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I. -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -o hmmerfm-exactmatch.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmerfm-exactmatch.c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmerfm-exactmatch.c:158:12: warning: absolute value function 'abs' given an argument of type 'int64_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] j += abs(fm->C[c]); ^ /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/hmmerfm-exactmatch.c:158:12: note: use function 'llabs' instead j += abs(fm->C[c]); ^~~ llabs 1 warning generated. cc -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -L../easel -L./impl_sse -L../libdivsufsort -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm ld: warning: easel.c(easel.o:(esl_FileTail) in archive ../easel/libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: easel.c(easel.o:(esl_FileConcat) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src' gmake -C profmark all gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/profmark' cc -I../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I../src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -o create-profmark.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/profmark/create-profmark.c cc -O2 -pipe -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm ld: warning: esl_alphabet.c(esl_alphabet.o:(esl_alphabet_CreateCustom) in archive ../easel/libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_sqio_ascii.c(esl_sqio_ascii.o:(esl_sqascii_Open) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() cc -I../easel -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/easel -I../src -I/exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src -O2 -pipe -pthread -fPIC -msse2 -DHAVE_CONFIG_H -o rocplot.o -c /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/profmark/rocplot.c cc -O2 -pipe -pthread -fPIC -DHAVE_CONFIG_H -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm ld: warning: esl_getopts.c(esl_getopts.o:(set_option) in archive ../easel/libeasel.a): warning: strcpy() is almost always misused, please use strlcpy() ld: warning: esl_getopts.c(esl_getopts.o:(esl_opt_SpoofCmdline) in archive ../easel/libeasel.a): warning: sprintf() is often misused, please use snprintf() gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/profmark' >>> Running package in biology/hmmer at 1731785180.07 ===> biology/hmmer ===> Faking installation for hmmer-3.1beta2p0 /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -d /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/bin /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -d /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/lib /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -d /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/include /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -d /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/man/man1 /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -d /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/share/doc/hmmer gmake -C src install gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src' gmake -C impl_sse install gmake[2]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src/impl_sse' for file in impl_sse.h; do \ /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0644 /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/impl_sse/$file /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/include/ ;\ done gmake[2]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src/impl_sse' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan hmmpgmd hmmc2 makehmmerdb hmmerfm-exactmatch; do \ /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0755 $file /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/bin/ ;\ done /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0755 libhmmer.a /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/lib/ for file in hmmer.h cachedb.h p7_gbands.h p7_gmxb.h p7_gmxchk.h p7_hmmcache.h; do \ /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0644 /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/src/$file /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/include/ ;\ done /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0644 p7_config.h /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/include/ ;\ gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/src' gmake -C documentation install gmake[1]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/documentation' gmake -C man install gmake[2]: Entering directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/documentation/man' for file in hmmer hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 0755 /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/documentation/man/$file.man /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/man/man1/${file}.1 ;\ done gmake[2]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/documentation/man' gmake[1]: Leaving directory '/exopi-obj/pobj/hmmer-3.1beta2/build-amd64/documentation' /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 644 /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/Userguide.pdf /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/share/doc/hmmer /exopi-obj/pobj/hmmer-3.1beta2/bin/install -d -m 755 /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/share/examples/hmmer /exopi-obj/pobj/hmmer-3.1beta2/bin/install -c -m 644 /exopi-obj/pobj/hmmer-3.1beta2/hmmer-3.1b2/tutorial/* /exopi-obj/pobj/hmmer-3.1beta2/fake-amd64/usr/local/share/examples/hmmer ===> Building package for hmmer-3.1beta2p0 Create /exopi-cvs/ports/packages/amd64/all/hmmer-3.1beta2p0.tgz Creating package hmmer-3.1beta2p0 reading plist| switching to /exopi-cvs/ports/biology/hmmer/pkg/PFRAG.amd64| checking dependencies| checksumming| checksumming| | 0% checksumming|* | 1% checksumming|** | 2% checksumming|** | 4% checksumming|*** | 5% checksumming|**** | 6% checksumming|***** | 7% checksumming|***** | 9% checksumming|****** | 10% checksumming|******* | 11% checksumming|******** | 12% checksumming|******** | 14% checksumming|********* | 15% checksumming|********** | 16% checksumming|*********** | 17% checksumming|*********** | 19% checksumming|************ | 20% checksumming|************* | 21% 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